I'm not sure I completely understand your question but I'll try to address it the best I can. From what I've heard/read you should not have any trouble with motor mounts when swapping in a late model five liter. Just pick up a set of standard 289 mounts from a 66 car (don't use the mounts from a 65 because they allow the engine to sit up higher than the 66's). With those, the motor should drop right in.
If you are going to use the AOD from the donor car, you're going to need a special tranny crossmember to get it to line up right. I believe Mustang's Plus (and several other venders) offers a kit for installing a late model transmission is an early car.
I'm willing to bet that you'll have to modify the drive shaft to make it fit, but do so after everything else is permenantly in place.
It sounds like a cool project.....Hope this helps
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1965 Coupe: 351W, comp cam, Aluminum Systemax II heads (2.02/1.60), 1.7 Cobra full roller rockers, Edelbrock intake, Holley 650 double pumper, Mallory Unilite, MSD-6AL, MSD Blaster 2 coil, MSD heli-core plug wires, Hedman headers, 2 1/2" exhaust (GT style) w/ 40 series delta flows, 69 C4 w/ shift kit, shelby traction bars, 3.55:1 rear
Daily Driver:
1989 GT- 5spd, K&N (no silencer), Shorty Headers, King Cobra Clutch, Flowmaster Force II Cat-back
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